Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 2JK8R

Calculation Name: 1HU3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HU3

Chain ID: A

ChEMBL ID:

UniProt ID: O43432

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2454473.272484
FMO2-HF: Nuclear repulsion 2368506.536645
FMO2-HF: Total energy -85966.735839
FMO2-MP2: Total energy -86210.029807


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:SER)


Summations of interaction energy for fragment #1(A:1:SER)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-0.901-0.2177.505-3.472-4.717-0.028
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.015
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A746PRO00.0320.0093.907-1.1320.020-0.002-0.456-0.6940.000
4A747GLU-1-0.766-0.8492.387-1.154-0.4790.967-0.621-1.0210.002
5A748ASN0-0.005-0.0042.039-5.582-6.8426.541-2.379-2.902-0.030
6A749ILE00.0320.0194.6251.1701.287-0.001-0.016-0.1000.000
7A750LYS10.9470.9597.3441.6751.6750.0000.0000.0000.000
8A751THR0-0.016-0.0025.9880.5010.5010.0000.0000.0000.000
9A752GLN00.0280.0438.4040.5480.5480.0000.0000.0000.000
10A753GLU-1-0.889-0.95410.549-0.682-0.6820.0000.0000.0000.000
11A754LEU0-0.051-0.01211.5380.1690.1690.0000.0000.0000.000
12A755PHE00.011-0.01210.8290.1130.1130.0000.0000.0000.000
13A756ARG10.9050.95114.0730.7340.7340.0000.0000.0000.000
14A757LYS10.8830.94215.3060.5630.5630.0000.0000.0000.000
15A758VAL00.0140.00316.9800.0610.0610.0000.0000.0000.000
16A759ARG10.8630.89417.4560.4500.4500.0000.0000.0000.000
17A760SER0-0.010-0.00320.1050.0510.0510.0000.0000.0000.000
18A761ILE0-0.049-0.02020.7940.0320.0320.0000.0000.0000.000
19A762LEU0-0.025-0.02521.0430.0250.0250.0000.0000.0000.000
20A763ASN00.0220.01623.2780.0220.0220.0000.0000.0000.000
21A764LYS10.8590.94625.0680.2570.2570.0000.0000.0000.000
22A765LEU00.0390.03228.9120.0050.0050.0000.0000.0000.000
23A766THR0-0.042-0.04531.9110.0140.0140.0000.0000.0000.000
24A767PRO0-0.030-0.00331.183-0.006-0.0060.0000.0000.0000.000
25A768GLN00.0510.04127.5010.0130.0130.0000.0000.0000.000
26A769MET00.0180.01030.9190.0000.0000.0000.0000.0000.000
27A770PHE00.061-0.00429.539-0.007-0.0070.0000.0000.0000.000
28A771ASN00.0370.01630.430-0.008-0.0080.0000.0000.0000.000
29A772GLN00.0310.01630.394-0.013-0.0130.0000.0000.0000.000
30A773LEU0-0.0100.01125.514-0.014-0.0140.0000.0000.0000.000
31A774MET00.0710.02425.818-0.019-0.0190.0000.0000.0000.000
32A775LYS10.9300.98425.7930.1470.1470.0000.0000.0000.000
33A776GLN0-0.007-0.00824.087-0.018-0.0180.0000.0000.0000.000
34A777VAL00.016-0.00421.124-0.029-0.0290.0000.0000.0000.000
35A778SER0-0.071-0.04720.894-0.015-0.0150.0000.0000.0000.000
36A779GLY00.0360.03621.0720.0000.0000.0000.0000.0000.000
37A780LEU0-0.077-0.03216.953-0.057-0.0570.0000.0000.0000.000
38A781THR00.0160.00113.0600.0260.0260.0000.0000.0000.000
39A782VAL0-0.014-0.01513.104-0.088-0.0880.0000.0000.0000.000
40A783ASP-1-0.773-0.8519.880-0.556-0.5560.0000.0000.0000.000
41A784THR00.0280.0067.8900.1540.1540.0000.0000.0000.000
42A785GLU-1-0.772-0.84611.000-0.112-0.1120.0000.0000.0000.000
43A786GLU-1-0.849-0.9328.312-0.524-0.5240.0000.0000.0000.000
44A787ARG10.7870.8405.8991.4991.4990.0000.0000.0000.000
45A788LEU00.027-0.00111.2340.0080.0080.0000.0000.0000.000
46A789LYS10.8620.93312.9700.4150.4150.0000.0000.0000.000
47A790GLY00.0130.01613.3450.0120.0120.0000.0000.0000.000
48A791VAL00.008-0.00314.3510.0260.0260.0000.0000.0000.000
49A792ILE0-0.013-0.00516.5940.0350.0350.0000.0000.0000.000
50A793ASP-1-0.807-0.90417.029-0.252-0.2520.0000.0000.0000.000
51A794LEU0-0.0180.00015.4320.0210.0210.0000.0000.0000.000
52A795VAL0-0.005-0.00819.3810.0260.0260.0000.0000.0000.000
53A796PHE0-0.015-0.02422.1970.0250.0250.0000.0000.0000.000
54A797GLU-1-0.872-0.90119.360-0.329-0.3290.0000.0000.0000.000
55A798LYS10.8410.90523.6010.2140.2140.0000.0000.0000.000
56A799ALA0-0.024-0.01025.5190.0160.0160.0000.0000.0000.000
57A800ILE0-0.092-0.04827.0870.0170.0170.0000.0000.0000.000
58A801ASP-1-0.882-0.92027.329-0.167-0.1670.0000.0000.0000.000
59A802GLU-1-0.791-0.88529.243-0.157-0.1570.0000.0000.0000.000
60A803PRO00.0310.02331.4530.0020.0020.0000.0000.0000.000
61A804SER0-0.0150.00733.0960.0050.0050.0000.0000.0000.000
62A805PHE00.0070.01131.5540.0070.0070.0000.0000.0000.000
63A806SER00.002-0.01530.625-0.004-0.0040.0000.0000.0000.000
64A807VAL00.0300.01131.183-0.003-0.0030.0000.0000.0000.000
65A808ALA00.0230.02730.4950.0010.0010.0000.0000.0000.000
66A809TYR00.007-0.01126.604-0.010-0.0100.0000.0000.0000.000
67A810ALA00.0250.02226.845-0.008-0.0080.0000.0000.0000.000
68A811ASN0-0.009-0.03428.7280.0040.0040.0000.0000.0000.000
69A812MET00.0130.02720.791-0.001-0.0010.0000.0000.0000.000
70A813CYS0-0.029-0.01324.171-0.011-0.0110.0000.0000.0000.000
71A814ARG10.9330.96325.2250.1050.1050.0000.0000.0000.000
72A815CYS0-0.0320.00124.9650.0090.0090.0000.0000.0000.000
73A816LEU00.014-0.00118.802-0.002-0.0020.0000.0000.0000.000
74A817VAL0-0.061-0.02021.9000.0030.0030.0000.0000.0000.000
75A818THR0-0.060-0.03224.4090.0200.0200.0000.0000.0000.000
76A819LEU0-0.0020.00118.397-0.009-0.0090.0000.0000.0000.000
77A820LYS10.8480.91419.1120.0310.0310.0000.0000.0000.000
78A821VAL00.0210.01814.215-0.009-0.0090.0000.0000.0000.000
79A822PRO0-0.011-0.00913.0760.0270.0270.0000.0000.0000.000
80A832ASN00.005-0.01218.2720.0020.0020.0000.0000.0000.000
81A833PHE00.0920.04020.379-0.003-0.0030.0000.0000.0000.000
82A834ARG10.9530.95222.1590.0700.0700.0000.0000.0000.000
83A835LYS10.8710.93718.4160.0250.0250.0000.0000.0000.000
84A836LEU0-0.006-0.00217.5380.0000.0000.0000.0000.0000.000
85A837LEU00.0310.02121.225-0.010-0.0100.0000.0000.0000.000
86A838LEU00.0520.03624.165-0.003-0.0030.0000.0000.0000.000
87A839ASN00.0170.00720.9630.0060.0060.0000.0000.0000.000
88A840ARG10.8120.90220.7230.1860.1860.0000.0000.0000.000
89A841CYS0-0.030-0.01423.314-0.004-0.0040.0000.0000.0000.000
90A842GLN00.0490.00926.7260.0020.0020.0000.0000.0000.000
91A843LYS10.8620.94318.8840.2220.2220.0000.0000.0000.000
92A844GLU-1-0.810-0.87925.086-0.140-0.1400.0000.0000.0000.000
93A845PHE00.0760.01527.9320.0030.0030.0000.0000.0000.000
94A846GLU-1-0.835-0.91227.706-0.036-0.0360.0000.0000.0000.000
95A847LYS10.8080.91326.4620.1090.1090.0000.0000.0000.000
96A848ASP-1-0.854-0.91129.208-0.060-0.0600.0000.0000.0000.000
97A849LYS10.8010.89531.9450.0500.0500.0000.0000.0000.000
98A850ALA0-0.0110.01530.8140.0040.0040.0000.0000.0000.000
99A881ALA00.0970.03738.7510.0010.0010.0000.0000.0000.000
100A882LYS10.9670.98636.4540.0430.0430.0000.0000.0000.000
101A883ASP-1-0.882-0.93438.301-0.047-0.0470.0000.0000.0000.000
102A884LYS11.0261.00135.5030.0820.0820.0000.0000.0000.000
103A885ALA0-0.011-0.00435.169-0.005-0.0050.0000.0000.0000.000
104A886ARG10.8480.92335.6410.0470.0470.0000.0000.0000.000
105A887ARG10.8340.91037.1980.0610.0610.0000.0000.0000.000
106A888ARG10.9020.94226.0230.1340.1340.0000.0000.0000.000
107A889SER00.009-0.00333.292-0.004-0.0040.0000.0000.0000.000
108A890ILE00.0200.01634.899-0.001-0.0010.0000.0000.0000.000
109A891GLY00.0200.00734.038-0.001-0.0010.0000.0000.0000.000
110A892ASN00.0260.00029.689-0.012-0.0120.0000.0000.0000.000
111A893ILE00.003-0.00132.120-0.002-0.0020.0000.0000.0000.000
112A894LYS10.8630.94034.9440.1000.1000.0000.0000.0000.000
113A895PHE0-0.009-0.01626.2770.0010.0010.0000.0000.0000.000
114A896ILE00.0270.00029.392-0.001-0.0010.0000.0000.0000.000
115A897GLY00.0760.02432.0460.0040.0040.0000.0000.0000.000
116A898GLU-1-0.857-0.91832.666-0.085-0.0850.0000.0000.0000.000
117A899LEU0-0.013-0.01327.6350.0010.0010.0000.0000.0000.000
118A900PHE00.005-0.00331.5180.0030.0030.0000.0000.0000.000
119A901LYS10.8730.92934.3800.0840.0840.0000.0000.0000.000
120A902LEU0-0.066-0.02431.3320.0020.0020.0000.0000.0000.000
121A903LYS10.8720.94932.7690.0560.0560.0000.0000.0000.000
122A904MET0-0.062-0.02127.973-0.001-0.0010.0000.0000.0000.000
123A905LEU0-0.043-0.01828.109-0.001-0.0010.0000.0000.0000.000
124A906THR00.0520.02331.5460.0010.0010.0000.0000.0000.000
125A907GLU-1-0.815-0.92834.243-0.043-0.0430.0000.0000.0000.000
126A908ALA0-0.041-0.01434.7150.0000.0000.0000.0000.0000.000
127A909ILE00.0290.01130.9340.0000.0000.0000.0000.0000.000
128A910MET00.0210.03934.144-0.005-0.0050.0000.0000.0000.000
129A911HIS00.0150.02537.0080.0010.0010.0000.0000.0000.000
130A912ASP-1-0.892-0.93634.455-0.046-0.0460.0000.0000.0000.000
131A913CYS0-0.080-0.04135.037-0.003-0.0030.0000.0000.0000.000
132A914VAL00.0180.00837.3860.0000.0000.0000.0000.0000.000
133A915VAL00.0280.01539.8840.0010.0010.0000.0000.0000.000
134A916LYS10.7990.89335.9620.0620.0620.0000.0000.0000.000
135A917LEU0-0.039-0.02739.280-0.001-0.0010.0000.0000.0000.000
136A918LEU00.009-0.00141.7820.0010.0010.0000.0000.0000.000
137A919LYS10.8140.92636.9980.0500.0500.0000.0000.0000.000
138A920ASN0-0.099-0.06440.6460.0000.0000.0000.0000.0000.000
139A921HIS00.0800.04844.194-0.003-0.0030.0000.0000.0000.000
140A922ASP-1-0.756-0.85944.223-0.053-0.0530.0000.0000.0000.000
141A923GLU-1-0.752-0.86546.682-0.045-0.0450.0000.0000.0000.000
142A924GLU-1-0.826-0.91041.786-0.067-0.0670.0000.0000.0000.000
143A925SER0-0.048-0.04342.542-0.004-0.0040.0000.0000.0000.000
144A926LEU00.0360.02243.5340.0000.0000.0000.0000.0000.000
145A927GLU-1-0.747-0.82745.410-0.056-0.0560.0000.0000.0000.000
146A928CYS0-0.057-0.03340.365-0.002-0.0020.0000.0000.0000.000
147A929LEU00.0040.00942.996-0.001-0.0010.0000.0000.0000.000
148A930CYS00.0110.00544.4490.0010.0010.0000.0000.0000.000
149A931ARG10.8700.92743.7660.0600.0600.0000.0000.0000.000
150A932LEU0-0.0260.00438.999-0.001-0.0010.0000.0000.0000.000
151A933LEU00.021-0.00542.6870.0000.0000.0000.0000.0000.000
152A934THR00.017-0.00145.5300.0020.0020.0000.0000.0000.000
153A935THR0-0.099-0.05641.657-0.001-0.0010.0000.0000.0000.000
154A936ILE0-0.031-0.02838.933-0.001-0.0010.0000.0000.0000.000
155A937GLY00.0330.01942.9280.0010.0010.0000.0000.0000.000
156A938LYS10.9880.98445.4570.0420.0420.0000.0000.0000.000
157A939ASP-1-0.898-0.93240.930-0.048-0.0480.0000.0000.0000.000
158A940LEU0-0.051-0.02839.4870.0020.0020.0000.0000.0000.000
159A941ASP-1-0.768-0.85943.121-0.026-0.0260.0000.0000.0000.000
160A942PHE00.1180.06544.0620.0020.0020.0000.0000.0000.000
161A943GLU-1-0.782-0.91046.534-0.023-0.0230.0000.0000.0000.000
162A944LYS10.8260.91345.4720.0170.0170.0000.0000.0000.000
163A945ALA0-0.057-0.01944.0200.0010.0010.0000.0000.0000.000
164A946LYS10.8500.93645.8590.0250.0250.0000.0000.0000.000
165A947PRO00.0820.04748.512-0.001-0.0010.0000.0000.0000.000
166A948ARG10.8980.94742.1980.0270.0270.0000.0000.0000.000
167A949MET00.0160.03044.821-0.002-0.0020.0000.0000.0000.000
168A950ASP-1-0.790-0.89448.207-0.023-0.0230.0000.0000.0000.000
169A951GLN0-0.048-0.00647.8960.0000.0000.0000.0000.0000.000
170A952TYR00.010-0.02842.6380.0000.0000.0000.0000.0000.000
171A953PHE00.018-0.00148.597-0.001-0.0010.0000.0000.0000.000
172A954ASN0-0.009-0.00551.8440.0010.0010.0000.0000.0000.000
173A955GLN0-0.027-0.01647.0660.0000.0000.0000.0000.0000.000
174A956MET0-0.012-0.00649.497-0.001-0.0010.0000.0000.0000.000
175A957GLU-1-0.777-0.85552.154-0.023-0.0230.0000.0000.0000.000
176A958LYS10.8890.92454.4930.0210.0210.0000.0000.0000.000
177A959ILE0-0.047-0.03249.8110.0000.0000.0000.0000.0000.000
178A960VAL0-0.012-0.00154.163-0.001-0.0010.0000.0000.0000.000
179A961LYS10.7760.87356.7490.0220.0220.0000.0000.0000.000
180A962GLU-1-0.809-0.88656.808-0.021-0.0210.0000.0000.0000.000
181A963ARG10.9370.97157.3640.0230.0230.0000.0000.0000.000
182A964LYS10.8420.92353.3280.0300.0300.0000.0000.0000.000
183A965THR00.0310.01552.170-0.001-0.0010.0000.0000.0000.000
184A966SER0-0.003-0.02653.6160.0020.0020.0000.0000.0000.000
185A967SER00.010-0.00556.3200.0000.0000.0000.0000.0000.000
186A968ARG10.8650.91348.7390.0500.0500.0000.0000.0000.000
187A969ILE00.0290.01049.5410.0000.0000.0000.0000.0000.000
188A970ARG10.8600.94253.1160.0300.0300.0000.0000.0000.000
189A971PHE00.0620.01956.0120.0010.0010.0000.0000.0000.000
190A972MET0-0.020-0.00449.2410.0000.0000.0000.0000.0000.000
191A973LEU00.015-0.01449.798-0.001-0.0010.0000.0000.0000.000
192A974GLN0-0.023-0.02352.8760.0010.0010.0000.0000.0000.000
193A975ASP-1-0.895-0.92753.396-0.037-0.0370.0000.0000.0000.000
194A976VAL0-0.003-0.00749.2430.0000.0000.0000.0000.0000.000
195A977ILE0-0.061-0.03452.2920.0010.0010.0000.0000.0000.000
196A978ASP-1-0.841-0.92154.835-0.027-0.0270.0000.0000.0000.000
197A979LEU00.0100.00151.0850.0010.0010.0000.0000.0000.000
198A980ARG10.7040.82350.7540.0280.0280.0000.0000.0000.000
199A981LEU0-0.017-0.00853.8310.0010.0010.0000.0000.0000.000
200A982CYS0-0.042-0.00856.9060.0010.0010.0000.0000.0000.000
201A983ASN0-0.047-0.03154.8640.0000.0000.0000.0000.0000.000
202A984TRP0-0.065-0.06248.271-0.002-0.0020.0000.0000.0000.000
203A985VAL0-0.072-0.02052.175-0.002-0.0020.0000.0000.0000.000
204A986SER00.0180.01053.8780.0000.0000.0000.0000.0000.000